[2023-06-26 23:34:24,209] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:34:24,215] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:34:24,215] [INFO] DQC Reference Directory: /var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference
[2023-06-26 23:34:25,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:34:25,531] [INFO] Task started: Prodigal
[2023-06-26 23:34:25,531] [INFO] Running command: gunzip -c /var/lib/cwl/stgbff1a3ab-92bd-4046-84cb-895f411e7c91/GCA_002310995.1_ASM231099v1_genomic.fna.gz | prodigal -d GCA_002310995.1_ASM231099v1_genomic.fna/cds.fna -a GCA_002310995.1_ASM231099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:34:30,784] [INFO] Task succeeded: Prodigal
[2023-06-26 23:34:30,784] [INFO] Task started: HMMsearch
[2023-06-26 23:34:30,784] [INFO] Running command: hmmsearch --tblout GCA_002310995.1_ASM231099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference/reference_markers.hmm GCA_002310995.1_ASM231099v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:34:31,039] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:34:31,040] [INFO] Found 6/6 markers.
[2023-06-26 23:34:31,068] [INFO] Query marker FASTA was written to GCA_002310995.1_ASM231099v1_genomic.fna/markers.fasta
[2023-06-26 23:34:31,069] [INFO] Task started: Blastn
[2023-06-26 23:34:31,069] [INFO] Running command: blastn -query GCA_002310995.1_ASM231099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference/reference_markers.fasta -out GCA_002310995.1_ASM231099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:34:31,683] [INFO] Task succeeded: Blastn
[2023-06-26 23:34:31,687] [INFO] Selected 20 target genomes.
[2023-06-26 23:34:31,687] [INFO] Target genome list was writen to GCA_002310995.1_ASM231099v1_genomic.fna/target_genomes.txt
[2023-06-26 23:34:31,702] [INFO] Task started: fastANI
[2023-06-26 23:34:31,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff1a3ab-92bd-4046-84cb-895f411e7c91/GCA_002310995.1_ASM231099v1_genomic.fna.gz --refList GCA_002310995.1_ASM231099v1_genomic.fna/target_genomes.txt --output GCA_002310995.1_ASM231099v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:34:43,067] [INFO] Task succeeded: fastANI
[2023-06-26 23:34:43,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:34:43,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:34:43,070] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:34:43,070] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-26 23:34:43,070] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-26 23:34:43,073] [INFO] DFAST Taxonomy check result was written to GCA_002310995.1_ASM231099v1_genomic.fna/tc_result.tsv
[2023-06-26 23:34:43,074] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:34:43,074] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:34:43,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference/checkm_data
[2023-06-26 23:34:43,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:34:43,107] [INFO] Task started: CheckM
[2023-06-26 23:34:43,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310995.1_ASM231099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310995.1_ASM231099v1_genomic.fna/checkm_input GCA_002310995.1_ASM231099v1_genomic.fna/checkm_result
[2023-06-26 23:35:07,252] [INFO] Task succeeded: CheckM
[2023-06-26 23:35:07,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.66%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:35:07,279] [INFO] ===== Completeness check finished =====
[2023-06-26 23:35:07,279] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:35:07,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310995.1_ASM231099v1_genomic.fna/markers.fasta)
[2023-06-26 23:35:07,280] [INFO] Task started: Blastn
[2023-06-26 23:35:07,280] [INFO] Running command: blastn -query GCA_002310995.1_ASM231099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e56ee3-9b7f-4bc5-9bd7-4a57e0806a92/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310995.1_ASM231099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:35:08,115] [INFO] Task succeeded: Blastn
[2023-06-26 23:35:08,120] [INFO] Selected 9 target genomes.
[2023-06-26 23:35:08,120] [INFO] Target genome list was writen to GCA_002310995.1_ASM231099v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:35:08,141] [INFO] Task started: fastANI
[2023-06-26 23:35:08,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff1a3ab-92bd-4046-84cb-895f411e7c91/GCA_002310995.1_ASM231099v1_genomic.fna.gz --refList GCA_002310995.1_ASM231099v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310995.1_ASM231099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:35:13,564] [INFO] Task succeeded: fastANI
[2023-06-26 23:35:13,582] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:35:13,582] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002310995.1	s__UBA1177 sp002310995	100.0	736	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.84	99.84	0.93	0.93	2	conclusive
GCA_902774115.1	s__UBA1177 sp902774115	86.7283	565	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	96.80	96.80	0.84	0.84	2	-
GCA_017645765.1	s__UBA1177 sp017645765	86.4849	560	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017963125.1	s__UBA1177 sp017963125	85.7277	566	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233945.1	s__UBA1177 sp905233945	84.9938	510	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405875.1	s__UBA1177 sp017405875	83.8766	519	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	97.50	97.50	0.88	0.88	2	-
GCA_002310035.1	s__UBA1177 sp002310035	83.373	368	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235605.1	s__UBA1177 sp905235605	83.2553	493	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.00	99.00	0.87	0.87	2	-
GCA_017538365.1	s__UBA1177 sp017538365	83.0162	513	738	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:35:13,585] [INFO] GTDB search result was written to GCA_002310995.1_ASM231099v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:35:13,585] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:35:13,590] [INFO] DFAST_QC result json was written to GCA_002310995.1_ASM231099v1_genomic.fna/dqc_result.json
[2023-06-26 23:35:13,590] [INFO] DFAST_QC completed!
[2023-06-26 23:35:13,590] [INFO] Total running time: 0h0m49s